404 papers
This study demonstrates that implementing sparse testing designs with genomic prediction models incorporating genotype-by-environment interactions can reduce Miscanthus breeding phenotyping costs by fivefold while maintaining predictive accuracy for biomass yield and related traits.
This study demonstrates that multi-trait multi-environment genomic prediction models significantly enhance the accuracy of selecting complex traits like total culm number and average internode length in *Miscanthus sacchariflorus* breeding programs, particularly for untested genotypes or missing data scenarios, thereby accelerating genetic gain despite variable performance across different traits.
By leveraging multi-modal epigenomic profiling across a telomere-to-telomere human genome reference, this study reveals that transposable elements, particularly SVA and specific Alu and LTR subfamilies, engage in an evolutionary arms race with host defense systems primarily by escaping H3K9me3-mediated heterochromatinization and progressively invading CTCF-rich regulatory regions to drive genomic innovation.
This study analyzes DNA from the 1978 Shroud of Turin samples to reveal a complex biological history comprising multiple human mitochondrial lineages, diverse epidermal and environmental microbes, and contaminants from various plants and animals, while also confirming that specific threads used for repairs date to 1534 and 1694 CE.
The paper introduces TEsingle, a computational tool that overcomes challenges in repetitive sequence alignment and intron retention to enable accurate, locus-specific analysis of transposable element expression in single-cell transcriptomes, revealing cell-type-specific TE dysregulation in Parkinson's disease.
This paper introduces muChIRP-seq, a low-input microfluidic technology that enables genome-scale profiling of lncRNA-chromatin interactions in as few as 50,000 cells, revealing distinct roles for specific lncRNAs and their coordination with epigenomic mechanisms in schizophrenia pathogenesis.
LongcallD is a unified framework that leverages long-read sequencing and local multiple-sequence alignment to simultaneously call and phase small variants, structural variants, and low-fraction mosaic variants, thereby overcoming the limitations of existing disconnected tools and improving accuracy in complex genetic analysis.
This study demonstrates that stress-responsive enhancer RNAs, particularly EN526, function as active intermediates linking chromatin reprogramming to post-transcriptional control of senescence by regulating CDKN2C stability and translation, thereby influencing cellular aging and disease phenotypes.
This study demonstrates that a streamlined, single-platform Oxford Nanopore workflow can generate reference-grade, diploid telomere-to-telomere genome assemblies and haplotype-resolved 3D chromatin maps for diverse individuals, eliminating the need for multi-platform sequencing strategies while achieving high accuracy and scalability.
This study presents a high-quality, near chromosome-scale genome assembly of the common pine sawfly (*Diprion pini*), generated using long-read and linked-read technologies without Hi-C sequencing, which provides a valuable resource for understanding its evolution, identifying unique genes related to plant metabolite processing, and developing improved pest management strategies.
This study demonstrates that BAF chromatin remodeling complexes are continuously required to maintain accessibility at stimulus-responsive "primed" enhancers, particularly those bound by AP-1 and lineage-defining transcription factors, thereby enabling the transcriptional responses to environmental cues like interferon gamma and dexamethasone.
An analysis of 1,001 European wolf genomes reveals a complex mosaic of distinct evolutionary lineages with varying levels of inbreeding and deleterious mutations, indicating that despite demographic recovery, many populations face significant genetic health risks that necessitate nuanced, region-specific conservation strategies.
This study integrates comparative genomics and Nano-tRNAseq across the Saccharomycotina subphylum to reveal lineage-specific diversity in tRNA sequences and modification enzymes, demonstrating that the loss of specific tRNA-modifying enzymes is associated with the absence of their target nucleotides in tRNA gene sequences.
This study reveals that the exceptional longevity and viral tolerance of Nearctic *Myotis* bats are driven by pleiotropic adaptations involving positive selection in DNA virus-interacting proteins and copy number variation in RNA virus-interacting proteins, alongside pervasive selection in cancer pathways and unique DNA damage responses.
The paper introduces causarray, a robust causal inference framework that leverages generalized confounder adjustment and semiparametric machine learning to accurately identify causal gene expression effects in single-cell and pseudo-bulk genomic data despite unmeasured confounders, as demonstrated in applications to autism and Alzheimer's disease studies.
This study establishes a cell-free system using Drosophila syncytial embryo extracts to demonstrate that complex chromatin architectures, including loops and topologically associating domains, can spontaneously reconstitute from soluble components, revealing that specific domain formation at the *eve* locus relies on direct boundary element pairing by the Su(Hw) protein rather than simple loop extrusion.
This study presents a high-quality, chromosome-scale genome assembly of sacha inchi and utilizes comparative genomics and transcriptome profiling to elucidate the molecular mechanisms driving its high alpha-linolenic acid content and triacylglycerol accumulation, thereby providing a critical foundation for future genetic improvement of this valuable oilseed crop.
This study demonstrates that incorporating weather covariates to identify environmentally correlated locations allows for the optimization of genomic prediction models for *Miscanthus sacchariflorus*, achieving high predictive accuracy with significantly reduced training sets and enabling more efficient resource allocation in breeding programs.
By integrating multi-scale evolutionary models to identify deleterious mutations, this study reveals that while domesticated sugar beets initially accumulated a higher genetic load than wild relatives, over a century of modern breeding has successfully purged these harmful variants, offering a refined set of targets for future crop improvement.
This study reveals that the invasive zebra and quagga mussels possess strikingly different sex determination architectures, with zebra mussels exhibiting a polygenic ZZ/ZW system and quagga mussels utilizing a localized XX/XY system driven by a novel male-determining *FoxL2-Y* locus, highlighting unexpected reproductive divergence and rapid evolutionary mechanisms in closely related invasive species.